Method of Characterization of Visible and/or Sub-Visible Particles in Biologics

ABSTRACT

A method for characterizing or quantifying one or more proteins in visible and/or sub-visible particles formed in a sample by detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

FIELD

The invention generally pertains to a method for characterizing or quantifying one or more proteins in visible and/or sub-visible particles formed in a sample.

BACKGROUND

Protein based biopharmaceutical products have emerged as important drugs for the treatment of cancer, autoimmune disease, infection and cardiometabolic disorders, and they represent one of the fastest growing product segments of the pharmaceutical industry. Robust and stable biopharmaceutical products are a key element in the successful delivery of in the biopharmaceutical industry. A key criterion is the development of formulations essentially free of visible and/or sub-visible particles. Visible and/or sub-visible particles, particularly in such protein based biopharmaceutical products, have been the focus of debate and investigation within the biopharmaceutical industry for several years. Consisting of synthetic or biological materials and originating from various sources, particles can raise the potential for immunogenic effects in patients and may have different effects on the drug product. Thus, it can be important to investigate the origin, composition, and consequences of these particles in order to help reduce or eliminate them from drug products.

When visible and/or sub-visible particles occur in biopharmaceutical products, identification of their composition is a critical step in understanding and mitigating their formation. However, this is a challenging task to determine the workflow and analytical tests since these particles are small, fragile, difficult to isolate, and composed of only a small mass of material. From the foregoing it will be appreciated that a need exists for improved methods for characterizing such visible and/or sub-visible particles that might be formed in a sample.

SUMMARY

A key criterion in developing biopharmaceuticals is to develop formulations that are free of visible and sub-visible particles. When such particles do occur, their identification and quantification can be an important step in the bioprocess.

Exemplary embodiments disclosed herein satisfy the aforementioned demands by providing methods for characterizing, identifying and/or quantifying protein(s) in at least one visible or sub-visible particle in a sample.

This disclosure, at least in part, provides a method for characterization of a protein in at least one visible or sub-visible particle in a sample.

In one exemplary embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample comprises detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise identifying presence of the protein in at least one visible or sub-visible particle using a Raman spectroscopy.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise at least one visible or sub-visible particle having a size of at least about 5 μm.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise at least one visible or sub-visible particle comprising an inherent impurity.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane with a pore size of about 5 μm.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in urea after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in guanidine hydrochloride after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for characterization a protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in 8 M urea solution after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can further comprise digesting the sample under denaturing conditions after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a protein of interest.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises an antibody.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a therapeutic antibody.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a nano liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise using a tandem mass spectrometer to characterize the protein.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a protein which is a host-cell protein.

This disclosure, at least in part, provides a method for identification of a protein in at least one visible or sub-visible particle in a sample.

In one exemplary embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample comprises detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise identifying presence of the protein in at least one visible or sub-visible particle using a Raman spectroscopy.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise at least one visible or sub-visible particle having a size of at least about 5 μm.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can be an inherent impurity.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane with a pore size of about 5 μm.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in urea after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in 8 M urea solution after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can further comprise digesting the sample under denaturing conditions after identifying the presence of a protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a protein of interest.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises an antibody.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a therapeutic antibody.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise a liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise a nano liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise using a tandem mass spectrometer to characterize the protein.

In one aspect of this embodiment, the method for identification of a protein in at least one visible or sub-visible particle in a sample can comprise a protein which is a host-cell protein.

This disclosure, at least in part, provides a method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample.

In one exemplary embodiment, the a method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample comprises detecting at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein to determine if the protein is the host cell-protein.

In one aspect of this embodiment, the identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise identifying the host-cell protein in at least one visible or sub-visible particle using a Raman spectroscopy.

In one aspect of this embodiment, the identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise at least one visible or sub-visible particle having a size of at least about 5 μm.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a host-cell protein which can be an inherent impurity.

In one aspect of this embodiment, the method of identification of a host cell-protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can further comprise capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane with a pore size of about 5 μm.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in urea after identifying the presence of a host-cell protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can further comprise dissolving the sample in 8 M urea solution after identifying the presence of a host-cell protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can further comprise digesting the sample under denaturing conditions after identifying the presence of a host-cell protein in the at least one visible or sub-visible particle.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a protein of interest.

In one aspect of this embodiment, the method for characterization of a protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises an antibody.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise a sample which further comprises a therapeutic antibody.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise a liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise a nano liquid chromatography system coupled to a mass spectrometer.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise using a tandem mass spectrometer to characterize the protein.

In one aspect of this embodiment, the method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample can comprise a protein which is a host-cell protein.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 shows the range of particle sizes of particles found in drug products (in microns).

FIG. 2 shows the types of particulate matter in drug products.

FIG. 3 shows a schematic scheme of common mechanism of protein aggregates.

FIG. 4 lists the potential causes of particle formation in drug products.

FIG. 5 shows the graph of FDA drug recalls due to particulate matter over the years 2005-2017.

FIG. 6 shows the chart showing the reasons for FDA sterile injectable drug recalls from the years 2008 to 2012.

FIG. 7 shows two workflows for characterization of a protein or host-cell protein according to an exemplary embodiment.

FIG. 8 shows a workflow for characterization of a protein or host-cell protein according to some exemplary embodiments.

FIG. 9 shows a method of capturing a visible or sub-visible particle according to one exemplary embodiment.

FIG. 10 shows excisions on filter paper made to evaluate a visible or sub-visible particle according to one exemplary embodiment.

FIG. 11 shows comparisons of abundance of peptide fragments of mAb1 in cut areas of filter paper used to capture a visible or sub-visible particle according to an exemplary embodiment.

FIG. 12 shows a method of capturing a visible or sub-visible particle according on a gold-coated polycarbonate membrane to an exemplary embodiment.

FIG. 13 shows a dark field illumination of particles analyzed using Raman spectroscopy isolated and captured according on a gold-coated polycarbonate membrane according to an exemplary embodiment.

FIG. 14 shows the relative abundance of metalloproteinase inhibitor 1 (TIMP1) in drug solutions from different lots (lots 5-12) analyzed according an exemplary embodiment.

FIG. 15 shows the relative abundance of C—C motif chemokine 13 (CCL13) in drug solutions from different lots (lots 5-12) analyzed according an exemplary embodiment.

FIG. 16 shows the relative quantitation of host-cell proteins identified in high molecular weight samples using targeted LC-MS/MS according to an exemplary embodiment.

FIG. 17 shows a method of capturing a visible or sub-visible particle according on a gold-filter according to an exemplary embodiment.

FIG. 18 shows a method of isolating a visible or sub-visible particle on a gold-filter according to an exemplary embodiment.

FIG. 19 shows the confirmation of presence of protein in a visible or sub-visible particle using Raman spectroscopy according to an exemplary embodiment.

FIG. 20 shows the abundance of mAb1 in particles characterized according to an exemplary embodiment.

FIG. 21 shows a dark-filled image of a sample comprising sub-visible particles taken according to an exemplary embodiment.

FIG. 22 shows a dark-filled image and Raman image of a sample comprising sub-visible particles taken according to an exemplary embodiment.

FIG. 23 shows a graph of decrease in Vmax capacity and turbidity over time for two filters used to characterize particles according to an exemplary embodiment.

FIG. 24 shows excision of filter paper carried out according to an exemplary embodiment.

FIG. 25 shows a graph of normalized abundance of heavy chain and light chain of mAb2 in particles over 72 hours for a particle comprising mAb2 carried out according to an exemplary embodiment.

FIG. 26 shows a parallel plot of relative abundance of host cell proteins versus time for a particle comprising mAb2 carried out according to an exemplary embodiment.

FIG. 27 shows a bubble plot of ratio of abundance of host-cell proteins in a particle at time T=0 hour to the host-cell proteins in the particle at time T=0 hour over relative amount of mAb2 in the particle at time T=0 hour carried out according to an exemplary embodiment.

FIG. 28 shows a bubble plot of ratio of abundance of host-cell proteins in a particle at time T=24 hour to the host-cell proteins in the particle at time T=0 hours over relative amount of mAb2 in the particle at time T=24 hours carried out according to an exemplary embodiment.

FIG. 29 shows a bubble plot of ratio of abundance of host-cell proteins in a particle at time T=48 hours to the host-cell proteins in the particle at time T=0 hour over relative amount of mAb2 in the particle at time T=48 hours carried out according to an exemplary embodiment.

FIG. 30 shows a bubble plot of ratio of abundance of host-cell proteins in a particle at time T=72 hours to the host-cell proteins in the particle at time T=0 hour over relative amount of mAb2 in the particle at time T=72 hours carried out according to an exemplary embodiment.

DETAILED DESCRIPTION

Presence of visible and sub-visible particles is a major issue during formulation of drug products comprising proteins. These particles can be either proteinaceous or non-proteinaceous and need to be analyzed to monitor the stability of the formulation. Increasing concerns about the immunogenic potential of such particles in drug products require a robust method and/or workflow to characterize its content.

A major challenge during formulation development of drug products comprising proteins, is overcoming their limited stability. Aggregation is one of the most serious degradation mechanisms. Aggregates can vary in many aspects such as size, reversibility, and structure. For instance, their size can range from dimers in the nanometer range to large aggregates of hundreds of microns, which are visible to the human eye (See FIG. 1). The aggregates can comprise proteinaceous as well as non-proteinaceous particles, for example, originating from packaging material or excipients influencing product quality and therefore need to be analyzed.

As disclosed in U.S. Pharmacopeia, the chapters designated for “Visible Particulates in Injections <790>” and “subvisible Particulate Matter in Therapeutic Protein Injections <1787>” aid in providing a general guidance on particulate matter content of drug products. The types of particulate matter that can be present in drug products are outlined in FIG. 2.

Inherent particulate matter in drug products as shown in FIG. 2 can comprise aggregated protein. The aggregation can be formed due to different types of different mechanisms and pathways (See FIG. 3). These mechanisms are not mutually exclusive and can occur in parallel within the same product (John Philo & Tsutomu Arakawa, Mechanisms of Protein Aggregation, 10 CURRENT PHARMACEUTICAL BIOTECHNOLOGY 348-351 (2009)). The predominant mechanisms depends not only on the protein itself, but also on a variety of other factors, such as the formulation, the presence of impurities or contaminants, and the exposure to chemical or physical stress mentioned above. It is currently not fully understood how different aggregation mechanisms and the thereby resulting structural differences of aggregates influence their potential immunogenicity.

Some of the potential causes of particle formation in drug products, listed in FIG. 4, are namely due to thermal stress, degradation during storage time, chemical degradation of the excipients in the drug product, mechanical stress, and interfacial stress. Potential consequences of such particles in drug products can render the product unsafe (cause capillary blood vessel occlusion, immunogenicity, or cytotoxicity), alter the efficacy (cause hypo- or hyper-potency or change the biodistribution and clearance of the drug in the body), alter the pharmacokinetics of the drug, render the product inconsistent, or render the bioprocess inconsistent.

FDA recalls of injectable drugs suggest that particulate matter is one of the main reasons for drug recalls (See FIG. 5). From the years 2008-2012, the presence of visible particles accounted for 22% of recalls among sterile injectable drugs (See FIG. 6).

Regulatory bodies require drug product analysis for particulate matter to include visible and sub-visible particle analysis as a part of product characterization and control and a risk assessment should be included to assess their potential impact on safety and efficacy. The analyses also involve multiple stress conditions for assessment of propensity to form particulate matter and stability evaluation. Following such analyses, strategies are required to be implemented to minimize the formation of particulate matter. For visible particles, the U. S. Pharmacopeia (U.S.P.) guidance on testing particulate matter lists (i) requirement of 100% visual inspection at filling process (USP <1> Injections), (ii) guidance for 100% visual inspection (USP <790> Visible Particulates in Injections), and (iii) description of inspector training, sampling methods, and inspection; emphasizes prevention/inspection lifecycle (USP <1790> Visual Inspection of Injections). The U. S. Pharmacopeia (U.S.P.) also lists guidance on testing particulate matter for sub-visible particles, such as, (i) the limits for sub-visible particles (≥10 μm particles ≤25 per ml; ≥25 μm particles ≤3 per ml) and recommendation of the two methods, light obscuration and microscopy, for particle counting (USP <788> Particulate Matter in Injections), (ii) specific requirement for Biologicals and discontinuation of use of microscopy for counting proteinaceous particles (USP <787> Subvisible Particulate Matter in Therapeutic Protein Injections), and (iii) methods to distinguish types of particles; emphasis on characterization of proteinaceous particles (USP <1787> Measurement of Subvisible Particulate Matter in Therapeutic Protein Injections). Lastly, for particulate Matter in Ophthalmic Solutions, the U. S. Pharmacopeia (U.S.P.) guidance on testing particulate matter provides guidance in chapters USP <789> Particulate Matter in Ophthalmic Solutions and USP <1788> Methods for the Determination of Particulate Matter in Injections and Ophthalmic Solutions.

One of the major challenges during protein formulation development and evaluation is characterization and quantification of potential degradation products, particularly aggregates and particles (Linda Narhi, Jeremy Schmit & Deepak Sharma, Classification of protein aggregates, 101 JOURNAL OF PHARMACEUTICAL SCIENCES 493-498 (2012)).

While instrument manufacturers have worked on providing new analytical techniques to overcome an analytical gap in the sub-visible size range, there is a large demand of establishing a workflow to aid their critical scientific evaluation.

Considering the limitations of existing methods, an effective and efficient method for identification and characterization of visible or sub-visible particles in a drug product was developed.

Unless described otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing, particular methods and materials are now described. All publications mentioned are hereby incorporated by reference.

The term “a” should be understood to mean “at least one”; and the terms “about” and “approximately” should be understood to permit standard variation as would be understood by those of ordinary skill in the art; and where ranges are provided, endpoints are included.

In some exemplary embodiments, the disclosure provides a method for characterization of a protein in at least one visible or sub-visible particle in a sample.

As used herein, the term “protein” includes any amino acid polymer having covalently linked amide bonds. Proteins comprise one or more amino acid polymer chains, generally known in the art as “polypeptides”. “Polypeptide” refers to a polymer composed of amino acid residues, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof linked via peptide bonds, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof. “Synthetic peptides or polypeptides’ refers to a non-naturally occurring peptide or polypeptide. Synthetic peptides or polypeptides can be synthesized, for example, using an automated polypeptide synthesizer. Various solid phase peptide synthesis methods are known to those of skill in the art. A protein may contain one or multiple polypeptides to form a single functioning biomolecule. A protein can include any of bio-therapeutic proteins, recombinant proteins used in research or therapy, trap proteins and other chimeric receptor Fc-fusion proteins, chimeric proteins, antibodies, monoclonal antibodies, polyclonal antibodies, human antibodies, and bispecific antibodies. In another exemplary aspect, a protein can include antibody fragments, nanobodies, recombinant antibody chimeras, cytokines, chemokines, peptide hormones, and the like. Proteins may be produced using recombinant cell-based production systems, such as the insect bacculovirus system, yeast systems (e.g., Pichia sp.), mammalian systems (e.g., CHO cells and CHO derivatives like CHO-K1 cells). For a review discussing biotherapeutic proteins and their production, see Ghaderi et al., “Production platforms for biotherapeutic glycoproteins. Occurrence, impact, and challenges of non-human sialylation,” (BIOTECHNOL. GENET. ENG. REV. 147-175 (2012)). In some exemplary embodiments, proteins comprise modifications, adducts, and other covalently linked moieties. Those modifications, adducts and moieties include for example avidin, streptavidin, biotin, glycans (e.g., N-acetylgalactosamine, galactose, neuraminic acid, N-acetylglucosamine, fucose, mannose, and other monosaccharides), PEG, polyhistidine, FLAGtag, maltose binding protein (MBP), chitin binding protein (CBP), glutathione-S-transferase (GST) myc-epitope, fluorescent labels and other dyes, and the like. Proteins can be classified on the basis of compositions and solubility and can thus include simple proteins, such as, globular proteins and fibrous proteins; conjugated proteins, such as, nucleoproteins, glycoproteins, mucoproteins, chromoproteins, phosphoproteins, metalloproteins, and lipoproteins; and derived proteins, such as, primary derived proteins and secondary derived proteins.

In some exemplary embodiments, the protein can be an antibody, a bispecific antibody, a multispecific antibody, antibody fragment, monoclonal antibody, host-cell protein or combinations thereof.

The term “antibody,” as used herein includes immunoglobulin molecules comprising four polypeptide chains, two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, as well as multimers thereof (e.g., IgM). Each heavy chain comprises a heavy chain variable region (abbreviated herein as HCVR or V_(H)) and a heavy chain constant region. The heavy chain constant region comprises three domains, C_(H)1, C_(H)2 and C_(H)3. Each light chain comprises a light chain variable region (abbreviated herein as LCVR or V_(L)) and a light chain constant region. The light chain constant region comprises one domain (C.sub.L1). The V_(H) and V_(L) regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FR). Each V_(H) and V_(L) is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. In different exemplary embodiments, the FRs of the anti-big-ET-1 antibody (or antigen-binding portion thereof) may be identical to the human germline sequences, or may be naturally or artificially modified. An amino acid consensus sequence may be defined based on a side-by-side analysis of two or more CDRs. The term “antibody,” as used herein, also includes antigen-binding fragments of full antibody molecules.

The terms “antigen-binding portion” of an antibody, “antigen-binding fragment” of an antibody, and the like, as used herein, include any naturally occurring, enzymatically obtainable, synthetic, or genetically engineered polypeptide or glycoprotein that specifically binds an antigen to form a complex. Antigen-binding fragments of an antibody may be derived, e.g., from full antibody molecules using any suitable standard techniques such as proteolytic digestion or recombinant genetic engineering techniques involving the manipulation and expression of DNA encoding antibody variable and optionally constant domains. Such DNA is known and/or is readily available from, e.g., commercial sources, DNA libraries (including, e.g., phage-antibody libraries), or can be synthesized. The DNA may be sequenced and manipulated chemically or by using molecular biology techniques, for example, to arrange one or more variable and/or constant domains into a suitable configuration, or to introduce codons, create cysteine residues, modify, add or delete amino acids, etc.

As used herein, an “antibody fragment” includes a portion of an intact antibody, such as, for example, the antigen-binding or variable region of an antibody. Examples of antibody fragments include, but are not limited to, a Fab fragment, a Fab′ fragment, a F(ab′)2 fragment, a Fc fragment, a scFv fragment, a Fv fragment, a dsFv diabody, a dAb fragment, a Fd′ fragment, a Fd fragment, and an isolated complementarity determining region (CDR) region, as well as triabodies, tetrabodies, linear antibodies, single-chain antibody molecules, and multi specific antibodies formed from antibody fragments. Fv fragments are the combination of the variable regions of the immunoglobulin heavy and light chains, and ScFv proteins are recombinant single chain polypeptide molecules in which immunoglobulin light and heavy chain variable regions are connected by a peptide linker. An antibody fragment may be produced by various means. For example, an antibody fragment may be enzymatically or chemically produced by fragmentation of an intact antibody and/or it may be recombinantly produced from a gene encoding the partial antibody sequence. Alternatively or additionally, an antibody fragment may be wholly or partially synthetically produced. An antibody fragment may optionally comprise a single chain antibody fragment. Alternatively or additionally, an antibody fragment may comprise multiple chains that are linked together, for example, by disulfide linkages. An antibody fragment may optionally comprise a multi-molecular complex.

The term “monoclonal antibody” as used herein is not limited to antibodies produced through hybridoma technology. A monoclonal antibody can be derived from a single clone, including any eukaryotic, prokaryotic, or phage clone, by any means available or known in the art. Monoclonal antibodies useful with the present disclosure can be prepared using a wide variety of techniques known in the art including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof.

As used herein, the term “host-cell protein” includes protein expressed by the host cell and can be unrelated to the desired protein of interest. Host-cell protein can be a process-related impurity which can be derived from the manufacturing process and can include the three major categories: cell substrate-derived, cell culture-derived and downstream derived. Cell substrate-derived impurities include, but are not limited to, proteins derived from the host organism and nucleic acid (host cell genomic, vector, or total DNA). Cell culture-derived impurities include, but are not limited to, inducers, antibiotics, serum, and other media components. Downstream-derived impurities include, but are not limited to, enzymes, chemical and biochemical processing reagents (e.g., cyanogen bromide, guanidine, oxidizing and reducing agents), inorganic salts (e.g., heavy metals, arsenic, nonmetallic ion), solvents, carriers, ligands (e.g., monoclonal antibodies), and other leachables.

In some exemplary embodiments, the at least one visible or sub-visible particle can comprise a process related impurity.

In some exemplary embodiments, the at least one visible or sub-visible particle can comprise a product related impurity.

As used herein, “product-related impurities” (e.g., precursors, certain degradation products) can be molecular variants arising during manufacture and/or storage that do not have properties comparable to those of the desired product with respect to activity, efficacy, and safety. Such variants may need considerable effort in isolation and characterization in order to identify the type of modification(s). Product-related impurities can include truncated forms, modified forms, and aggregates. Truncated forms are formed by hydrolytic enzymes or chemicals which catalyze the cleavage of peptide bonds. Modified forms include, but are not limited to, deamidated, isomerized, mismatched S—S linked, oxidized, or altered conjugated forms (e.g., glycosylation, phosphorylation). Modified forms can also include any post-translational modification form. Aggregates include dimers and higher multiples of the desired product. (Q6B Specifications: Test Procedures and Acceptance Criteria for Biotechnological/Biological Products, ICH August 1999, U.S. Dept. of Health and Humans Services).

In some exemplary embodiments, the visible or sub-visible particle can comprise protein aggregate. As used herein, the term “protein aggregate” refers to assemblies of protein monomers which can vary in size, reversibility, and structure. Some of the mechanisms of protein aggregate formation are outlined in FIG. 4.

As used herein, the term “formulation” refers to an active pharmaceutical agent that is formulated together with one or more pharmaceutically acceptable vehicles.

As used herein, the term “an active pharmaceutical agent” can include a biologically active component of a drug product. An active pharmaceutical agent can refer to any substance or combination of substances used in a drug product, intended to furnish pharmacological activity or to otherwise have direct effect in the diagnosis, cure, mitigation, treatment or prevention of disease, or to have direct effect in restoring, correcting or modifying physiological functions in animals. Non-limiting methods to prepare an active pharmaceutical agent can include using fermentation process, recombinant DNA, isolation and recovery from natural resources, chemical synthesis, or combinations thereof.

In some exemplary embodiments, the formulation can be a protein formulation.

As used herein, the term “protein formulation” refers to a therapeutic protein that is formulated together with one or more pharmaceutically acceptable vehicles. In some embodiments, the therapeutic protein is present in a unit dose amount appropriate for administration in a therapeutic regimen.

In some other embodiments, the formulation can further comprise excipients including, but not limited to buffering agents, bulking agents, tonicity modifiers, surfactants, solubilizing agents, and preservatives. Other additional excipients can also be selected based on function and compatibility with the formulations may be found, for example in LOYD V. ALLEN, REMINGTON: THE SCIENCE AND PRACTICE OF PHARMACY (19 ed. 1995), JOHN E HOOVER, REMINGTON'S PHARMACEUTICAL SCIENCES (1975), and LYOD ALLEN, ANSEL'S PHARMACEUTICAL DOSAGE FORMS AND DRUG DELIVERY SYSTEMS (10 ed.) herein incorporated by reference in their entirety.

In some exemplary embodiments, the formulation can be stable.

The stability of a formulation can comprise evaluating the chemical stability, physical stability or functional stability of the active pharmaceutical agent. The formulations of the present invention typically exhibit high levels of stability of the active pharmaceutical agent.

In terms of protein formulations, the term “stable,” as used herein, refers to the proteins within the formulations that can retain an acceptable degree of chemical structure or biological function after storage under exemplary conditions described herein. A formulation may be stable even though the protein contained therein does not maintain 100% of its chemical structure or biological function after storage for a defined amount of time. Under certain circumstances, maintenance of about 90%, about 95%, about 96%, about 97%, about 98% or about 99% of a protein's structure or function after storage for a defined amount of time may be regarded as “stable”.

In some exemplary embodiments, the fatty acid particles can be at least 5 μm in size. Further, these fatty acid particles can be classified according to their size as visible (>100 μm), sub-visible (<100 μm, which can be sub-divided into micron (1-100 μm) and submicron (100 nm-1000 nm)) and nanometer particles (<100 nm) (Linda Narhi, Jeremy Schmit & Deepak Sharma, Classification of protein aggregates, 101 JOURNAL OF PHARMACEUTICAL SCIENCES 493-498 (2012)).

In some exemplary embodiments, the particles can be detected as protein by Raman Spectroscopy. As used herein, the term “Raman spectroscopy” refers to a spectroscopic method based on Raman scattering method. Raman Spectroscopy can provide a Raman spectrum, which can identify the presence and position of bands in the fingerprint region (2000 to 400 cm⁻¹) which enables the chemical identification of the analyzed material by comparison with a database of Raman spectra (C. V. Raman and K. S. Krishnan, A new type of secondary radiation, 121 NATURE 501-502 (1928); Zai-Qing Wen, Raman spectroscopy of protein pharmaceuticals, 96 JOURNAL OF PHARMACEUTICAL SCIENCES 2861-287 (2007)).

As used herein, the term “chromatography” refers to a process in which a chemical mixture carried by a liquid or gas can be separated into components as a result of differential distribution of the chemical entities as they flow around or over a stationary liquid or solid phase. Non-limiting examples of chromatography include traditional reversed-phased (RP), ion exchange (IEX) and normal phase chromatography (NP). Unlike RP, NP and IEX chromatography, in which hydrophobic interaction, hydrophilic interaction and ionic interaction respectively are the dominant interaction modes, mixed-mode chromatography can employ a combination of two or more of these interaction modes.

As used herein, the term “mass spectrometer” includes a device capable of identifying specific molecular species and measuring their accurate masses. The term is meant to include any molecular detector into which a polypeptide or peptide may be eluted for detection and/or characterization. A mass spectrometer can include three major parts: the ion source, the mass analyzer, and the detector. The role of the ion source is to create gas phase ions. Analyte atoms, molecules, or clusters can be transferred into gas phase and ionized either concurrently (as in electrospray ionization). The choice of ion source depends heavily on the application.

As used herein, the term “mass analyzer” includes a device that can separate species, that is, atoms, molecules, or clusters, according to their mass. Non-liming examples of mass analyzers that could be employed for fast protein sequencing are time-of-flight (TOF), magnetic/electric sector, quadrupole mass filter (Q), quadrupole ion trap (QIT), orbitrap, Fourier transform ion cyclotron resonance (FTICR), and also the technique of accelerator mass spectrometry (AMS).

As used herein, the term “tandem mass spectrometry” includes a technique where structural information on sample molecules is obtained by using multiple stages of mass selection and mass separation. A prerequisite is that the sample molecules can be transferred into gas phase and ionized intact and that they can be induced to fall apart in some predictable and controllable fashion after the first mass selection step. Multistage MS/MS, or MS^(n), can be performed by first selecting and isolating a precursor ion (MS²), fragmenting it, isolating a primary fragment ion (MS³), fragmenting it, isolating a secondary fragment (MS⁴), and so on as long as one can obtain meaningful information or the fragment ion signal is detectable. Tandem MS has been successfully performed with a wide variety of analyzer combinations. What analyzers to combine for a certain application can be determined by many different factors, such as sensitivity, selectivity, and speed, but also size, cost, and availability. The two major categories of tandem MS methods are tandem-in-space and tandem-in-time, but there are also hybrids where tandem-in-time analyzers are coupled in space or with tandem-in-space analyzers. A tandem-in-space mass spectrometer comprises an ion source, a precursor ion activation device, and at least two non-trapping mass analyzers. Specific m/z separation functions can be designed so that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyzer for m/z separation and data acquisition. In tandem-in-time, mass spectrometer ions produced in the ion source can be trapped, isolated, fragmented, and m/z separated in the same physical device.

The peptides identified by the mass spectrometer can be used as surrogate representatives of the intact protein and their post translational modifications. They can be used for protein characterization by correlating experimental and theoretical MS/MS data, the latter generated from possible peptides in a protein sequence database. The characterization includes, but is not limited, to sequencing amino acids of the protein fragments, determining protein sequencing, determining protein de novo sequencing, locating post-translational modifications, or identifying post translational modifications, or comparability analysis, or combinations thereof.

As used herein, the term “database” refers to bioinformatic tools which provide the possibility of searching the uninterpreted MS-MS spectra against all possible sequences in the database(s). Non-limiting examples of such tools are Mascot (http://www.matrixscience.com), Spectrum Mill (http://www.chem.agilent.com), PLGS (http://www.waters.com), PEAKS (http://www.bioinformaticssolutions.com), Proteinpilot (http://download.appliedbiosystems.com//proteinpilot), Phenyx (http://www.phenyx-ms.com), Sorcerer (http://www.sagenresearch.com), OMSSA (http://www.pubchem.ncbi.nlm.nih.gov/omssa/), X!Tandem (http://www.thegpm.org/TANDEM/), Protein Prospector (http://www. http://prospector.ucsf.edu/prospector/mshome.htm), Byonic (https://www.proteinmetrics.com/products/byonic) or Sequest (http://fields.scripps.edu/sequest).

EXEMPLARY EMBODIMENTS

Embodiments disclosed herein provide compositions, methods, and systems for the rapid characterization of proteins in a sample.

In some exemplary embodiments, this disclosure provides a method for characterization of a protein in at least one visible or sub-visible particle in a sample, comprising detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

In some exemplary embodiments, this disclosure provides a method for identification of a protein in at least one visible or sub-visible particle in a sample, comprising detecting the at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein.

In some exemplary embodiments, this disclosure provides a method for identification of a host cell-protein in at least one visible or sub-visible particle in a sample, comprising detecting at least one visible or sub-visible particle in the sample, isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein, and using a mass spectrometer to characterize the protein to determine if the protein is the host cell-protein.

In some exemplary embodiments, Raman spectroscopy can be used to identify the presence of the protein in at least one visible or sub-visible particle.

In some exemplary embodiments, the at least one visible or sub-visible particle can have a size of at least about 2 μm. In one aspect, the at least one visible or sub-visible particle can have a size of at least about 2 μm, at least about 3 μm, at least about 4 μm, at least about 5 μm, at least about 6 μm, at least about 7 μm, at least about 8 μm, at least about 9 μm, at least about 10 μm, at least about 11 μm, at least about 12 μm, at least about 13 μm, at least about 14 μm, at least about 15 μm, at least about 20 μm, at least about 25 μm, at least about 30 μm, at least about 35 μm, at least about 40 μm, at least about 45 μm, at least about 50 μm, at least about 55 μm, at least about 60 μm, at least about 65 μm, at least about 70 μm, at least about 7 μm, at least about 80 μm, at least about 85 μm, at least about 90 μm, at least about 95 μm, or at least about 100 μm.

In some exemplary embodiments, the protein can be an inherent impurity.

In some exemplary embodiments, the at least one visible or sub-visible particle can be captured on a gold-coated polycarbonate membrane. In some exemplary embodiments, the gold-coated polycarbonate membrane can have a pore size of about 5 μm.

In some exemplary embodiments, the at least one visible or sub-visible particle can be captured on a filter paper. In some exemplary embodiments, the filter paper can have a pore size of about 5 μm.

In some exemplary embodiments, the method can further comprise excising a portion of a gold-coated polycarbonate membrane or a filter paper used to capture the at least one visible or sub-visible particle.

In some exemplary embodiments, the method can further comprise dissolving the sample in urea after identifying the presence of a protein or a host-cell protein in the at least one visible or sub-visible particle. In one aspect, the sample can be dissolved in 8 M urea solution.

In some exemplary embodiments, the method can further comprise denaturing the sample under denaturing conditions after identifying the presence of a protein or a host-cell protein in the at least one visible or sub-visible particle. In one aspect, the sample can be denatured using dithiothreitol at a suitable temperature.

In some exemplary embodiments, the method can further comprise digesting the sample under denaturing conditions after identifying the presence of a protein or a host-cell protein in the at least one visible or sub-visible particle. In one aspect, the sample can be digested using a hydrolyzing agent. Non-limiting examples of hydrolyzing agents that can carry out enzymatic digestion include trypsin, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, outer membrane protease T (OmpT), immunoglobulin-degrading enzyme of Streptococcus pyogenes (IdeS), chymotrypsin, pepsin, thermolysin, papain, pronase, and protease from Aspergillus Saitoi. Non-limiting examples of hydrolyzing agents that can carry out non-enzymatic digestion include the use of high temperature, microwave, ultrasound, high pressure, infrared, solvents (non-limiting examples are ethanol and acetonitrile), immobilized enzyme digestion (IMER), magnetic particle immobilized enzymes, and on-chip immobilized enzymes. For a recent review discussing the available techniques for protein digestion see Switazar et al., “Protein Digestion: An Overview of the Available Techniques and Recent Developments” (J. Proteome Research 2013, 12, 1067-1077). One or a combination of hydrolyzing agents can cleave peptide bonds in a protein or polypeptide, in a sequence-specific manner, generating a predictable collection of shorter peptides.

In some exemplary embodiments, the sample can further comprise a protein of interest. In one aspect, the protein of interest can be a therapeutic antibody, an antibody, a monoclonal antibody, a polyclonal antibody, a bispecific antibody, an antibody fragment, a fusion protein, or combination thereof.

In one exemplary embodiment, the protein or host-cell protein can be a post-translationally modification of protein of interest. The various post-translational modifications include, but are not limited to, cleavage, N-terminal extensions, protein degradation, acylation of the N-terminus, biotinylation (acylation of lysine residues with a biotin), amidation of the C-terminal, glycosylation, iodination, covalent attachment of prosthetic groups, acetylation (the addition of an acetyl group, usually at the N-terminus of the protein), alkylation (the addition of an alkyl group (e.g. methyl, ethyl, propyl) usually at lysine or arginine residues), methylation, adenylation, ADP-ribosylation, covalent cross links within, or between, polypeptide chains, sulfonation, prenylation, Vitamin C dependent modifications (proline and lysine hydroxylations and carboxy terminal amidation), Vitamin K dependent modification wherein Vitamin K is a cofactor in the carboxylation of glutamic acid residues resulting in the formation of a γ-carboxyglutamate (a glu residue), glutamylation (covalent linkage of glutamic acid residues), glycylation (covalent linkage glycine residues), glycosylation (addition of a glycosyl group to either asparagine, hydroxylysine, serine, or threonine, resulting in a glycoprotein), isoprenylation (addition of an isoprenoid group such as farnesol and geranylgeraniol), lipoylation (attachment of a lipoate functionality), phosphopantetheinylation (addition of a 4′-phosphopantetheinyl moiety from coenzyme A, as in fatty acid, polyketide, non-ribosomal peptide and leucine biosynthesis), phosphorylation (addition of a phosphate group, usually to serine, tyrosine, threonine or histidine), and sulfation (addition of a sulfate group, usually to a tyrosine residue). The post-translational modifications that change the chemical nature of amino acids include, but are not limited to, citrullination (the conversion of arginine to citrulline by deimination), and deamidation (the conversion of glutamine to glutamic acid or asparagine to aspartic acid). The post-translational modifications that involve structural changes include, but are not limited to, formation of disulfide bridges (covalent linkage of two cysteine amino acids) and proteolytic cleavage (cleavage of a protein at a peptide bond). Certain post-translational modifications involve the addition of other proteins or peptides, such as ISGylation (covalent linkage to the ISG15 protein (Interferon-Stimulated Gene)), SUMOylation (covalent linkage to the SUMO protein (Small Ubiquitin-related MOdifier)) and ubiquitination (covalent linkage to the protein ubiquitin). See http://www.uniprot.org/docs/ptmlist for a more detailed controlled vocabulary of PTMs curated by UniProt.

In another exemplary embodiment, the sample can be obtained from any step of the bioprocess, such as, culture cell culture fluid (CCF), harvested cell culture fluid (HCCF), process performance qualification (PPQ), any step in the downstream processing, drug solution (DS), or a drug product (DP) comprising the final formulated product. In some other specific exemplary embodiments, the sample can be selected from any step of the downstream process of clarification, chromatographic purification, viral inactivation, or filtration. In one aspect, the drug product can be selected from manufactured drug product in the clinic, shipping, storage, or handling.

In some exemplary embodiments, the mass spectrometer can be coupled to a liquid chromatography. In one aspect, the mass spectrometer can be coupled to a nano liquid chromatography. In some exemplary embodiments, the mobile phase used to elute the protein in liquid chromatography can be a mobile phase that can be compatible with a mass spectrometer. In one aspect, the mobile phase can be ammonium acetate, ammonium bicarbonate, or ammonium formate, or combinations thereof.

In another exemplary embodiment, the mass spectrometer can comprise a nanospray.

In some exemplary embodiments, the mass spectrometer can be a tandem mass spectrometer to characterize the protein.

In some exemplary embodiments, the protein or host-cell protein can be a therapeutic antibody, an antibody, a monoclonal antibody, a polyclonal antibody, a bispecific antibody, an antibody fragment, a fusion protein, or combinations thereof. In one aspect, the antibody fragment can include Fab fragment, a Fab′ fragment, a F(ab′)2 fragment, a scFv fragment, a Fv fragment, a dsFv diabody, a dAb fragment, a Fd′ fragment, a Fd fragment, and an isolated complementarity determining region (CDR) region, triabodies, tetrabodies, linear antibodies, single-chain antibody molecules, and multi specific antibodies formed from antibody fragments.

In some exemplary embodiments, the protein or host-cell protein can be a digestion product of the antibody. The digestion product can be formed by a hydrolyzing agent. The digestion product can be a product-related impurity.

In some exemplary embodiments, the protein or host-cell protein can have a pI in the range of about 4.5 to about 9.0. In one exemplary specific embodiment, the protein can have a pI of about 4.5, about 5.0, about 5.5, about 5.6, about 5.7, about 5.8, about 5.9, about 6.0, about 6.1 about 6.2, about 6.3, about 6.4, about 6.5, about 6.6, about 6.7, about 6.8, about 6.9, about 7.0, about 7.1 about 7.2, about 7.3, about 7.4, about 7.5, about 7.6, about 7.7, about 7.8, about 7.9, about 8.0, about 8.1 about 8.2, about 8.3, about 8.4, about 8.5, about 8.6, about 8.7, about 8.8, about 8.9, or about 9.0.

In one exemplary embodiment, the number of visible or sub-visible particles in the sample can be at least two.

In one exemplary embodiment, the types of protein or host-cell protein in the visible or sub-visible particle can be at least two.

It is understood that the methods are not limited to any of the aforesaid protein, impurity, column and that the methods for identifying or quantifying may be conducted by any suitable means.

In some exemplary embodiments, the disclosure provides a workflow comprising a particle inspection 100, particle isolation 110, particle capture 120, and a mass spectrometer 140 coupled to the chromatographic column 130 (See FIG. 7).

In some exemplary embodiments, the workflow can further comprise Raman spectroscopy 150 capable of identifying presence of a protein.

In some exemplary embodiments, the particle inspection 100 can be performed by visual inspection, light obscuration, or micro flow imaging. In one exemplary embodiment, the particle inspection can be performed by visual inspection, FTIR spectroscopy, Raman spectroscopy, or micro flow imaging (MFI).

In some exemplary embodiments, the particle isolation 110 and particle capture 120 can be carried out using filtration devices.

In some exemplary embodiments, the chromatographic column 130 can be capable of being washed with a mobile phase. In one exemplary embodiment, the mobile phase can be ammonium acetate, ammonium bicarbonate, or ammonium formate, or combinations thereof.

In some exemplary embodiments, the mass spectrometer 140 can comprise a nanospray.

In some exemplary embodiments, the mass spectrometer 140 can be a tandem mass spectrometer. In one exemplary embodiment, the mass spectrometer 140 can be a tandem in space mass spectrometer. In one exemplary embodiment, the mass spectrometer 140 can be a tandem in time mass spectrometer.

An exemplary embodiment of the workflow in displayed in FIG. 8.

It is understood that the system is not limited to any of the aforesaid protein, host-cell protein, spectroscopy method, or chromatographic column.

The consecutive labeling of method steps as provided herein with numbers and/or letters is not meant to limit the method or any embodiments thereof to the particular indicated order.

Various publications, including patents, patent applications, published patent applications, accession numbers, technical articles and scholarly articles are cited throughout the specification. Each of these cited references is herein incorporated by reference, in its entirety and for all purposes.

The disclosure will be more fully understood by reference to the following Examples, which are provided to describe the disclosure in greater detail. They are intended to illustrate and should not be construed as limiting the scope of the disclosure.

EXAMPLES Example 1

1.1 Detection of Particles

On evaluation of vials in a process performance qualification (PPQ) lot (lot no. 1) comprising mAb1 formulation, about 264 vials (˜4.5%) of the PPQ lot had visible particles. Since, the acceptable limit for the PPQ lot is 0.7%, the lot was rejected.

The PPQ lot was evaluated for the presence of polysorbate level, which was found to be normal.

A particle (particle 1) from the PPQ lot was captured on a grey filter (See FIG. 9).

1.2 Isolation of the Particle

Excisions were made on the filter paper: (a) cut area 1—a 4 mm×4 mm area where the particle 1 was loaded, (b) cut area 2—a 4 mm×4 mm area where the protein solution was loaded, and (c) cut are 3—a 4 mm×4 mm area where no protein was loaded (See FIG. 10). The cut areas/samples were dissolved in 8 M urea.

The samples were incubated with 8 M urea and 5 mM dithiothreitol (DTT) at 50° C. for 30 minutes, followed by incubation with 10 mM indole-3-acetic acid (IAA) at RT for 30 minutes. The incubate samples were digested with 1 μg of rLysC for 1 hour under denaturing condition, followed by dilution with Tris-HCl. To this mixture, 1 μg of trypsin was added and the digestion was continued for 3 hours. The digestion mixture was then acidified with 20% formic acid (FA) followed by nanoLC-MS/MS analysis.

1.3 Peptide Analysis

To find out the composition of particle 1, peptide analysis of particle 1 was carried out using nanoLC-MS/MS Thermo EASY-nLC coupled to Thermo QExactive HF mass spectrometer. The identity of the proteins present, the Proteome Discoverer v. 1.4 software using the Sequest mode was used by searching mass spectral data against a CHO protein sequence database. Peptide quality scores were derived by processing against a decoy database using the Peptide Validator node within Proteome Discoverer that calculates the probability that the search algorithm incorrectly included a peptide in a sample. The false discovery rate (FDR), or the false positive rate, is a statistical value that estimates the number of false positive identifications among all identifications found by a peptide identification search. Peptides assessed with less than 5% FDR (medium and high confidence peptides) were retained, and those assessed with less than a 1% FDR (high confidence) threshold noted as high confidence. A minimum of two medium or high confidence (passing) peptides per protein were required to positively identify each HCP. The MS/MS spectra of peptides for those proteins which were identified by only one high confidence peptide were manually examined for coverage of three or more consecutive b- and γ-ions and low number of abundant extraneous ions to determine their acceptance.

All the samples were analyzed for the abundance of mAb1. The cut area 1 (comprising particle 1) showed a high abundance of the mAb1 protein, followed by some presence of mAb1 in cut area 2 (protein solution without particle 1), and cut area 3 showed a low/absence of the mAb1 protein (See FIG. 11).

A host-cell protein other than mAb1—TIMP1 was found to be present in particle 1 (Table 1). However, TIMP1 was not present in the protein solution without particle 1 indicating that it was enriched in the particle.

TABLE 1 # of Unique Peptides Samples Protein ID Description Identified Cut Area 1 mAb1 HC 37 (Particle) mAb1 LC 22 TIMP1 Metalloproteinase 4 inhibitor 1 UniProt ID: P01033 Cut Area 2 mAb1 HC 31 (Protein mAb1 LC 16 Loading) Cut Area 3 mAb1 HC 22 (Negative mAb1 LC 11 Control)

Example 2

Four additional particles (particles 2-5) were identified in the PPQ lot (lot no. 1) containing the formulation from mAb1. These particles were captured and analyzed.

2.1 Isolation of the Particle

Each detected particle was placed on an individual Rap ID gold-coated polycarbonate membrane with a pore size of 5 μM and 40/20 nm coating as shown in FIG. 12.

Excisions were made on the membranes to isolate the particle from the protein solution, as illustrated in example 1.

2.2 Raman Analysis

Raman spectroscopy was employed to identify constituents of the particles. This method uses inelastic light scattering to generate an energy spectrum unique to each molecule, which is then compared to a reference library containing the fingerprints of various chemical structures. The Raman analysis confirmed that all four particles (particle 2, 3, 4 and 5) comprised protein. A dark field illumination showed that the particles surrounding areas has no or very minimal protein signals, which ensures that cutting particles form the filter did not induce contamination for MS analysis (See FIG. 13).

2.3 Peptide Analysis

To find out the composition of the particles, the peptide analysis of the particle was carried out using nanoLC-MS/MS as illustrated in example 1. Table 2 lists the host-cell proteins identified in particle 1 through 5, along with a drug solution lot (DS), all of which comprise mAb1. The host-cell proteins were screened using the regular nanoLC-MS/MS and confirmed using targeted nanoLC-MS/MS. Particles 3 and 4 were smaller in size and had about 10-50 times less protein amount that particle 1 and particle 5, which likely explains the result of less host-cell proteins being identified.

TABLE 2 Protein Proteins identified ID Description DS P1 P2 P3 P4 P5 mAb1 HC Y Y Y Y Y Y mAb1 LC Y Y Y Y Y Y TIMP1 Metalloproteinase inhibitor 1 N Y Y N N Y UniProt ID: P01033 PPIB Peptidyl-prolyl N N Y N N Y cis-trans isomerase B UniProt ID: P23284 ITIH5 Inter-alpha-trypsin N N Y N N Y inhibitor heavy chain H5 UniProt ID: Q86UX2 PPIC Peptidyl-prolyl N N Y N N Y cis-trans isomerase C UniProt ID: P45877 ALDOA Fructose-bisphosphate N N Y N N Y aldolase A UniProt ID: P04075 ANXA1 Annexin Al N N Y N N Y UniProt ID: P04083 CFL1 Cofilin-1 N N Y N N N UniProt ID: P23528 PTGR1 Prostaglandin reductase 1 N N Y N N N UniProt ID: F5GY50 CCL13 C-C motif chemokine 13 N N Y N N Y UniProt ID: Q99616 S100-A11 Protein S100-A11 N N Y N N N UniProt ID: P31949

The study confirmed the presence of host-cell proteins in the particle isolated rejected mAb1 lot no. 1.

Example 3

To study if visible particles were enriched with host-cell proteins in other lots comprising mAb1 formulation, particles in a clinical lot comprising mAb1 formulation (lot no. 2) and two other PPQ lots comprising mAb1 formulation (lot nos. 3 and 4) lots were evaluated.

The isolation of particles, Raman analysis and peptide analysis was performed as illustrated in Example 2.

Table 3 lists the host-cell proteins identified in particles from lot no. 1 (a PPQ lot), lot no. 2 (a clinical lot), lot no. 3 (a PPQ lot), and lot no. 4 (a PPQ lot). The host-cell proteins were screened using the regular nanoLC-MS/MS and confirmed using targeted nanoLC-MS/MS. Some host-cell proteins were not identified in the initial screening but were identified using confirmatory assays. Particles in lot no. 2 (clinical lot) were smaller in size and had about 15-30 times less protein amount than particles from lot no. 4 (PPQ lot), which likely explains the result of less host-cell proteins being identified. Comparing the host-cell proteins identified to be present in the particles from these lots 2-4 suggests that the proteins identified in the visible particles isolated from the lot no. 1 are comparable.

TABLE 3 Identified Confirmed Protein Lot no. Lot no. ID Description 1 2 3 4 1 2 3 4 mAb1 Heavy Chain Y Y Y Y Y Y Y Y mAb1 Light Chain Y Y Y Y Y Y Y Y TIMP1 Metalloproteinase inhibitor 1 Y N N Y Y N N Y UniProt ID: P01033 PPIB Peptidyl-prolyl cis-trans Y N N Y Y Y N Y isomerase B UniProt ID: P23284 ITIH5 Inter-alpha-trypsin Y N N Y Y N N Y inhibitor heavy chain H5 UniProt ID: Q86UX2 PPIC Peptidyl-prolyl cis-trans Y N N Y Y N N Y isomerase C UniProt ID: P45877 ALDOA Fructose-bisphosphate Y N N Y Y N N Y aldolase A UniProt ID: P04075 ANXA1 Annexin Al Y N N Y Y N N Y UniProt ID: P04083 CFL1 Cofilin-1 Y N N N Y N N Y UniProt ID: P23528 CCL13 C-C motif chemokine 13 Y N N Y Y Y N Y UniProt ID: Q99616 S100-A11 Protein S100-A11 Y N N N Y N N Y UniProt ID: P31949 ANXA2 Annexin A2 N N N Y — Y Y Y UniProt ID: HOYMU9 AK2 Adenylate kinase 2, N N N Y — N N Y mitochondrial″ UniProt ID: P54819 ST3GAL1 CMP-N-acetylneuraminate- N N N Y — N N Y beta-galactosamide- alpha-2,3-sialyltransferase 1″ UniProt ID: Q11201 GSTM2 Glutathione S-transferase Mu 2 N N N Y — N N Y UniProt ID: P28161

Example 4

To study if drug solution of mAb1 which could make up the PPQ lots is enriched with host-cell proteins, drug solution lots (lot nos. 5-12) were evaluated.

4.1 PLBD2 Levels

The drug solution was tested for PLBD2 using LC-MS MRM method using Hamster putative phospholipase B-like 2 (PLBD2) ELISA kit, catalog CSB-EL018125Ha from CUSABIO. This kit claims to provide quantitative determination of hamster putative phospholipase B-like (PLBD2) concentrations. A standard curve was generated showing detection of the hamster PLBL2 standard included in the kit over the range of 0.12-8 ng/ml. Drug solution from lot no.s 5-12 demonstrated PLBD2 level below the lower limit of quantitation (1 ppm i.e., 1 ng of PLBD in 1 mg mAb1)

Thus, drug solution in all of the above lots showed absence of abnormal PLBD2 levels.

4.2 HCP Profiling Using Direct Peptide Mapping

To find out the composition of the drug solution, peptide analysis was carried out using nanoLC-MS/MS as illustrated in example 1. The host-cell proteins were screened using the regular nanoLC-MS/MS and confirmed using targeted nanoLC-MS/MS. No host-cell proteins were identified in the any of the lots tested (lot nos. 5-12) (Table 4). TIMP1 and CCL13 were not identified in the initial screening of all the lots but were found to be present in the all the lots using more sensitive confirmatory assays. The relative abundance of the host cell proteins TIMP1 and CCL13 in drug solutions from lots 5-12 were plotted as normalized to relative abundance in lot no. 5 (See FIGS. 14 and 15).

Among the eight lots, lot no. 9 and lot no. 11 comprised drug solutions used to prepare the PPQ lots 1 and 3, respectively. The host cell proteins in the drug solutions in lot nos. 9 and 11 compared to the PPQ lots that they are used for suggests that there was not evaluated levels of host cell proteins observed in the lot that generated the particles compared to other drug substance lots.

TABLE 4 Identified Confirmed Protein ID Description proteins proteins mAb1 Heavy Chain Detected Detected mAb1 Light Chain TIMP1 Metalloproteinase inhibitor 1 Not Detected Detected UniProt ID: P01033 CCL13 C-C motif chemokine 13 UniProt ID: Q99616 PPIB Peptidyl-prolyl cis-trans Not Detected isomerase B UniProt ID: P23284 ITIH5 Inter-alpha-trypsin inhibitor heavy chain H5 UniProt ID: Q86UX2 PPIC Peptidyl-prolyl cis-trans isomerase C UniProt ID: P45877 ALDOA Fructose-bisphosphate aldolase A UniProt ID: P04075 ANXA1 Annexin A1 UniProt ID: P04083 CFL1 Cofilin-1 UniProt ID: P23528 PTGR1 Prostaglandin reductase 1 UniProt ID: F5GY50 S100-A11 Protein S100-A11 UniProt ID: P31949 ANXA2 Annexin A2 UniProt ID: H0YMU9 AK2 Adenylate kinase 2, mitochondrial″ UniProt ID: P54819 ST3GAL1 CMP-N-acetylneuraminate-beta- galactosamide-alpha-2,3- sialyltransferase 1″ UniProt ID: Q11201 GSTM2 Glutathione S-transferase Mu 2 UniProt ID: P28161

4.3 HCP Profiling Using Anti-HCP Immunopurification (IP) Enrichment Followed by Peptide Mapping

To further evaluate the host cell proteins present in the drug solution lots, a more sensitive anti-HCP immunopurification was carried out. A pool of biotinylated anti-HCP antibodies was used to pull-down and enriched HCPs by removing the therapeutic proteins and other components. Following the enrichment, the HCPs were then digested by enzyme and injected on NanoLC-MS for HCP identification and quantification. The enrichment allows us to more sensitively identify and quantify HCPs.

Table 5 lists the host cell proteins which were identified by performing HCP profiling using anti-HCP immunopurification enrichment.

TABLE 5 Gene # of peptide spectrum matches for each lot MW calc. ID Protein 5 6 7 8 9 10 11 12 [kDa] pI TIMP1 Metalloproteinase 33 23 28 28 37 25 32 35 22.4 8.47 inhibitor 1 GSTM6 Glutathione S- 19 15 28 23 31 24 20 22 86.5 8.21 transferase Mu 6 PPIB Peptidyl-prolyl cis-trans 9 7 10 5 8 3 5 4 23.6 9.58 isomerase B ITIH5 Inter-alpha-trypsin 5 3 5 8 7 2 7 4 102.0 8.60 inhibitor heavy chain H5 CCL13 C-C motif chemokine 6 5 5 5 5 0 5 7 15.8 9.16 PRDX1 Peroxiredoxin-1 3 0 6 9 2 5 7 6 22.2 7.72 ANXA 1 Annexin A1 4 0 6 4 3 2 0 0 38.8 7.02 CXCL3 C-X-C motif chemokine 4 0 4 2 3 0 0 2 11.0 8.81 GSTP1 Glutathione S-transferase P 2 4 2 2 5 0 0 0 25.0 8.12 DDT D-dopachrome 2 2 3 2 2 0 0 2 13.1 7.14 decarboxylase CTSZ Cathepsin Z 0 2 2 3 2 0 0 3 34.0 7.58 SIAE Sialate O-acetylesterase 0 0 3 3 2 0 0 2 61.4 8.22 B2M Beta-2-microglobulin 0 0 0 0 3 0 0 4 6.39 5.81 C1RA Complement C1r-A 2 0 3 0 0 0 0 0 80.05 6.06 subcomponent CTSL Cathepsin L1 0 0 2 0 0 0 2 0 37.22 7.17

Comparing the host cell proteins identified in lot no. 1 (PPQ lot, Table 5) to lot no. 9 (drug solution lot used to prepare the lot no. 1, Table 3), it can be concluded that no unique host cell protein is associated with the lot no. 1. This suggests that the host cell protein profile in the PPQ lot was similar to the host cell protein profile in the drug solution lot.

Example 5

The host-cell proteins could be enriched as a consequence of aggregate formation. This was studied by comparing the host-cell proteins in drug solution lot (lot no. 6) with lots enriched with high molecular weight species of mAb1 as represented in table 6 below.

TABLE 6 Lot no. Sample Description 6 DS control with mAb1 13 Total HMW (contains 93% total HMW material of mAb1) 14 Dimer (contains 90% dimer of mAb1) 15 vHMW (contains 92% vHMW material of mAb1)

The isolation of particles and Raman analysis for lots 13-15 was performed as illustrated in Example 2.

5.1 Host Cell Proteins Identified Using Direct Peptide Mapping

The samples were dried down using SpeedVac, and then dissolved by 8M Urea and 10 mM TCEP-HCl, and denatured at 50° C. for 30 minutes, followed by incubation with 10 mM indole-3-acetic acid (IAA) at RT for 30 minutes. The incubate samples were digested with 1 μg of rLysC for 1 hour under denaturing condition, followed by dilution with Tris-HCl. To this mixture, 1 μg of trypsin was added and the digestion was continued for 3 hours. The digestion mixture was then acidified with 20% formic acid (FA) followed by nanoLC-MS/MS analysis. Six host cell proteins were identified in the lot with enriched HMW mAb1 species, but not in the drug solution lot (Table 7).

TABLE 7 Identified in the lot Protein ID Description 6 13 14 15 TIMP1 Metalloproteinase inhibitor 1 Yes Yes GST-Mu 7 Glutathione S-Transferase Mu7 Yes PRDX1 Peroxiredoxin Yes Yes LDH L-lactate dehydrogenase Yes ANXA1 Annexin A1 Yes H2A Histone H2A Type 1 Yes

5.2 Relative Quantitation of Host Cell Proteins Using Targeted LC-MS/NIS

The identified peptide/protein from Step 5.1 above was used to create a mass list of identified peptides in order for the mass spectrometer to look for these specific peptides to fragment to further confirm and quantify the HCPs. In doing so, the detection sensitivity was increased due to the targeted screening. Seven host cell proteins were identified in the lots with enriched HMW mAb1 species (lot nos. 13-15). The amount of the host cell proteins identified in the lots with enriched HMW mAb1 species was about 2-60 fold higher than the amount of the host cell proteins in the drug solution lot (lot no. 6). FIG. 16 shows a chart of relative quantitation of host cell proteins in the lots with enriched HMW mAb1 species.

5.3 Host Cell Proteins Identified Using Anti-HCP IP Enrichment Followed by Peptide Mapping

A pool of biotinylated anti-HCP antibodies was used to pull-down and enriched HCPs by removing the therapeutic proteins and other components. Following the enrichment, the HCPs were then digested by enzyme and injected on NanoLC-MS for HCP identification and quantification. Thirty one host cell proteins were identified in the lots with enriched HMW mAb1 species (lot nos. 13-15). Out of thirty one host cell proteins, the drug solution lot only showed the presence of two host cell proteins (Table 8).

TABLE 8 # of peptide spectrum matches for each mAb1 lot MW calc. # Accession Protein Name 6 13 14 15 [kDa] pI 1 G3IBHO Metalloproteinase inhibitor 1 13 74 74 23 22.39 8.47 2 G3IKC3 Glutathione S-transferase Mu 6 10 75 69 30 86.50 8.21 3 G3HXN7 Beta-hexosaminidase 0 70 83 14 60.06 7.36 4 G3ILF3 Glutathione S-transferase Mu 7 0 22 26 0 25.86 7.37 5 G3GYP9 Peroxiredoxin-1 0 15 15 7 22.22 7.72 6 G3IIB1 Sialate O-acetylesterase 0 8 16 0 61.38 8.22 7 G3I5L3 Annexin A1 0 11 6 2 38.84 7.02 8 G3I5Z5 Prostaglandin reductase 1 0 9 8 0 42.59 6.27 9 G3H533 Peptidyl-prolyl cis-trans 0 6 5 0 23.62 9.58 isomerase 10 G3I6T1 Putative phospholipase B-like 2 0 0 10 4 65.50 6.28 11 G3INC5 Cathepsin L1 0 7 5 0 37.22 7.17 12 G3HY03 D-dopachrome decarboxylase 0 6 5 0 13.12 7.14 13 G3GTT2 C-C motif chemokine 0 7 3 0 15.85 9.16 14 G3I3K5 G-protein coupled receptor 56 0 7 2 0 77.32 8.82 15 G3GUR1 Complement C1r-A 0 3 5 0 80.05 6.06 subcomponent 16 G31EU2 Protein DJ-1 0 4 3 0 19.92 6.79 17 G3HCL3 Tumor necrosis factor ligand 0 3 3 0 33.63 6.24 superfamily member 9 18 G3I3V6 Discoidin, CUB and LCCL 0 2 3 0 73.60 7.49 domain-containing protein 2 19 G3GRS9 N-acetylgalactosamine-6- 0 3 3 0 53.99 6.93 sulfatase 20 G3I664 Procollagen C-endopeptidase 0 4 0 0 55.19 8.13 enhancer 1 21 G3HDU7 Histone H4 0 2 0 2 10.82 11.50 22 G31255 L-lactate dehydrogenase 0 3 0 0 42.15 8.43 23 G3GZZO Aspartate aminotransferase 0 3 0 0 46.22 7.21 24 G3HOS7 Beta-2-microglobulin 0 2 1 0 6.39 5.81 25 G3H8V4 Phospholipid transfer protein 0 3 0 0 54.34 6.65 26 G3GS02 10-formyltetrahydrofolate 0 0 0 2 96.16 5.90 dehydrogenase 27 G3HNJ3 Clusterin 0 0 0 0 51.72 5.74 28 G3HGM6 N(4)-(Beta-N- 0 0 2 0 37.21 7.46 acetylglucosaminyl)-L- asparaginase 29 G3H8V5 Carboxypeptidase 0 0 1 0 54.19 6.11 30 G3HCX3 Deoxyribonuclease-2-alpha 0 1 0 0 40.38 7.55 31 G3I3Y6 Glutathione S-transferase P 0 1 0 0 24.98 8.12

The above results show a higher amount and enrichment of host cell proteins in lots with HMW mAb1 species than mAb1 drug solution lot. This suggests that host cell proteins are enriched BMW mAb1 species.

Example 6

Drug product comprising mAb1 was also tested for the presence of visible particles and host cell proteins, in addition to testing drug solution of mAb1, lot comprising HMW species of mAb1 and PPQ lots of mAb1.

6.1 Detection of Particles

Two vials (vial #1 and vial #2) comprising the drug product—containing a mAb1 was inspected manually to detect the presence of a particle(s).

6.2 Isolation of the Particle

For each of the vial, the detected particle was placed on an individual (Rap ID) gold-coated polycarbonate membrane with a pore size of 5 μM and 40/20 nm coating as shown in FIG. 17.

Excisions were made on the membranes: (a) particle sample—a 3 mm diameter circular area with the particle(s) was excised and (b) negative control—a 3 mm diameter circular area without the particle was excised (FIG. 18). The particle sample and negative sample were dissolved in 8 M urea. Three particle samples and two negative controls were isolated from the membranes for the two vials as represented in Table 9.

TABLE 9 Source Vial# Gold Filter# Samples Vial#1 Filter#1 Filter#1 Particle#1 Filter#1 Control Vial#2 Filter#2 Filter#2 Particle#1 Filter#2 Particle#2 Filter#2 Control

6.3 Raman Analysis

Raman spectroscopy was performed on the particles as illustrated in example 2. The Raman spectra of one of the particle 1 as recited in table 9 confirmed that the particles were proteinaceous (See FIG. 19). The green trace as seen in FIG. 19 is the protein reference spectrum and the red trace as seen in FIG. 19 is the particle sample spectrum.

6.4 Peptide Analysis

Peptide analysis was performed on the particles as illustrated in example 2.

All the particle samples and negative samples were analyzed for the abundance of mAb1. The particle samples showed a high abundance of the mAb1 protein and negative samples showed absence of the mAb1 protein (See FIG. 20). The abundance peaks were estimated based on the averaged peak areas of the top 2 most abundant peptides in mAb1.

Proteins other than mAb1 obtained from the peptide analysis are represented in table 10. The mAb1 abundance in the particle samples and negative samples was normalized to 1E6 to relatively quantify the other proteins in ppm in Table 10. The term ND in table 10 is to represent that the protein was not detected.

TABLE 10 Abundances of HCP relative to DS in each sample (ppm) Vial#1 (Filter#1) Vial#2/Filter#2 Protein ID Paritcle#1 Control Paritcle#1 Paritcle#2 Control mAb1 1E6 1E6 1E6 1E6 1E6 G3IBH0 1229 ND 366  328 ND G3I4H6/ 115 ND 81  93 ND A0A061IB69 G3I5L3/ 60 ND ND ND ND A0A061I6Z5 G3H533 339 ND ND ND ND G3HKB0 90 ND ND ND ND G3H928 169 ND ND ND ND G3ILF3 83 ND ND ND ND G3GTT2 ND² ND 62 ND ND

The presence of protein in the particle samples and negative samples is shown in table 11.

TABLE 11 Particle Samples Negative Controls Filter#1 Filter#2 Filter#2 Filter#1 Filter#2 UniProt ID Paritcle#1 Paritcle#1 Paritcle#2 Control Control mAb1 Y Y Y Y Y G3IBH0 Y Y Y G3I4H6/ Y Y Y A0A061IB69 G3I5L3/ Y Y A0A061I6Z5 G3H533 Y Y G3HKB0 Y Y G3H928 Y G3ILF3 Y G3GTT2 Y

The peptide analysis revealed the presence of host-cell proteins in the particle isolated from drug product containing mAb1.

Example 7

Detection of sub-visible particles was also performed using a Formulated Drug Substance (FDS) comprising mAb1.

In order to isolate sub-visible particles, 1.5 ml of the FDS solution was pipetted on a gold-coated polycarbonate membrane with a pore size of 5 μM and 40/20 nm coating. This was then washed with milli-Q water. A particle free negative control was established for comparison by initially pipetting 1.5 ml of the FDS solution on a 0.2 μM filter (Millipore) and the flow-through was collected. The flow-through was then pipetted on a gold-coated polycarbonate membrane with a pore size of 5 μM and 40/20 nm coating and washed with milli-Q water.

Raman analysis and peptide analysis was performed as described in Example 2. The particles comprising protein were identified using the Raman spectroscopy. The dark-filled images of the particles comprising proteins identified by the recited method is shown in FIG. 21. The peptide analysis of the sub-visible particles demonstrated the presence of a host cell protein—Metalloproteinase inhibitor 1 along with mAb1, whereas the particle free negative control showed only the presence of mAb1. The absence of the host protein Metalloproteinase inhibitor 1 in the particle free negative control suggests that the host cell proteins were enriched in the sub-visible particles only (Table 12).

Detected by nanoLC-MS/MS Sub-Visible Particle-Free Protein ID Description Particles Negative Control mAb1 Heavy Chain Yes Yes mAb1 Light Chain Yes Yes TIMP1 Metalloproteinase Yes No inhibitor 1 UniProt ID: P01033

Example 8

To evaluate the presence of host cell proteins in bioprocess, harvested cell culture fluid (HCCF) from Preclinical Manufacturing and Process Development (PMPD) for mAb2 was tested. The HCCF for mAb2 showed presence of particles after sterile filtration and on freeze-thaw cycle. During the HCCF sterilizing filtration step at Industrial Operations and Product Supply (TOPS), high back pressure was experiences, indicating some non-soluble materials were clogging the filter.

The isolation of particles, Raman analysis and peptide analysis was performed as illustrated in Example 2. FIG. 22 shows a dark filled image and a Raman image of the particles. Other than mAb2, 743 host cell proteins were identified in one of the particles. The top ten HCPs (based on sequence coverage) were L-lactate dehydrogenase (UniProt Accession: Q06BU8), Actin, cytoplasmic (UniProt Accession: G3GVD0), Transketolase (UniProt Accession: G3GUU5), Rab GDP dissociation inhibitor beta (UniProt Accession: G3GR73), Glyceraldehyde-3-phosphate dehydrogenase (UniProt Accession: P17244), V-type proton ATPase catalytic subunit A (UniProt Accession: G3H066), Transgelin (UniProt Accession: G3H7Z2), Glutathione S-transferase Mu 5 (UniProt Accession: G3ILF1), Chloride intracellular channel protein 4 (UniProt Accession: G3HMU4), and Leukotriene A-4 hydrolase (UniProt Accession: G3HBI9).

Example 9

Particles comprised of host cell proteins at different steps in bioprocess can be lead to decrease in filter capacity. To assess the presence of host cell proteins in bioprocess, cell culture fluid (CCF) for mAb3/mAb2 bioprocess was tested.

9.1 Filter Capacity Assessment

The PMPD and the TOPS processes exhibited an abnormally low CCF filtration throughput in a few lots from various programs. For the one of the mAb3/mAb2 lot, harvest pool filter capacity was assessed after incubated for 0, 24, 48, and 72 hours at room temperature. The filter capacity assessment was performed using the Vmax method on the CCF filter pool at the above mentioned time points (Vmax™ Constant Pressure Test Protocol, Merck Millipore). In the Vmax™ test, the time and volume collected up to that time were recorded at regular intervals. The data was then plotted as time/volume versus time.

Two types of filters were used for the assessment—Sartopore® 2 (two layers of filters with 0.45 μm and 0.2 μm, respectively.) and LifeASSURE™ (two layers of filters with 0.65 μm and 0.2 μm, respectively)). The plot of Vmax capacity (L/m²) vs. time in hours (See FIG. 23) showed a decrease in Vmax™ over time, indicating aggregation or particle formation over time. The increase in time also showed an increase in turbidity. This increase in turbidity and decrease in filter capacity could be due to precipitation of host cell proteins or drug solution over time clogging the filters.

9.2 Protein Abundance Quantitation

To find out the cause of the increase in turbidity and decrease in filter capacity, CCF for mAb2 (pI: ˜6.3) was incubated pre-filtration for 0, 24, 48 and 72 hours at pH 5.60-6.10. The incubated CCF fluid at each time points was filtered using LifeASSURE™ filter (two layers of filters with 0.65 μm and 0.2 μm, respectively).

To evaluate what proteins precipitated over time, the filters were cut open and 4 mm discs were analyzed (See FIG. 24). The cut filter was immersed into 8M Urea and 10 mM TCEP-HCl and incubated at 50° C. for 30 minutes to dissolve, denature, and reduce the protein on the cut filter. The samples were then incubated with 10 mM indole-3-acetic acid (IAA) at RT for 30 minutes. The incubate samples were digested with 1 μg of rLysC for 1 hour under denaturing condition, followed by dilution with Tris-HCl. To this mixture, 1 μg of trypsin was added and the digestion was continued for 3 hours. The digestion mixture was then acidified with 20% formic acid (FA) followed by nanoLC-MS/MS analysis. The protein abundance was based on the average of mass spectrometry signal abundance of the top three peptide ions that assigned to a specific protein.

A total of 2366 quantifiable proteins were identified in the CCF of mAb2. From the identified proteins, 1880 proteins were included for further analysis (486 proteins were excluded because they showed less than two unique peptides per protein). The most abundant protein was mAb2. The abundance for mAb2 on the filter did not change over time (See FIG. 25 and Table 13).

TABLE 13 Ratio Ratio Ratio Ratio Protein T0/T0 T24/T0 T48/T0 T72/T0 mAb2 LC 1.00 1.02 1.28 1.42 mAb2 HC 1.00 0.93 0.91 0.79

The average abundance of mAb2 LC was set to 1E6 and abundance of other proteins was calculated using HCP peptide mass spectrometer peak areas were normalized against the average abundance of mAb2 LC. The top fifty most abundant proteins (listed in Table 14) were closely examined since they are more likely to clog the filters.

TABLE 14 Ratio of MW Calc. Relative Amount to mAb2 LC (ppm) T24 T48 T72 # Accession Description (Kda) pI T0 T24 T48 T72 /T0 /T0 /T0 1 mAb2 LC mAb2 LC 23.5 8.29 849424.3 864288.0 1083370.2 1202917.5 1.0 1.3 1.4 2 mAb2 HC mAb2 HC 48.9 6.37 506563.6 469802.7 460417.7 398929.1 0.9 0.9 0.8 3 G3I1V3 Fibronectin 273.3 5.44 27041.7 30534.9 64162.5 125338.2 1.1 2.4 4.6 4 Q9EPP7 Cathepsin Z 34.0 6.68 5524.6 5194.9 57941.1 104908.8 0.9 10.5 19.0 5 G3HNJ3 Clusterin 51.7 5.51 34533.8 36067.1 50770.9 56806.0 1.0 1.5 1.6 6 G3IBF4 Serine protease 28.7 6.54 12754.5 11588.1 37433.8 56748.6 0.9 2.9 4.4 HTRA1 7 G3GVD0 Actin, cytoplasmic 1 41.7 5.29 12927.6 16207.9 36190.2 47771.6 1.3 2.8 3.7 8 Q9WV24 Beta-2-microglobulin 13.8 7.08 5227.7 5978.0 18710.8 44490.9 1.1 3.6 8.5 9 G3IBHO Metalloproteinase 22.4 8.74 1637.8 1482.0 14522.5 36234.4 0.9 8.9 22.1 inhibitor 1 10 P17244 Glyceraldehyde-3- 35.7 8.49 14332.1 17828.0 25183.3 29354.1 1.2 1.8 2.0 phosphate dehydrogenase 11 G3H1W4 Tubulointerstitial 52.5 6.73 16774.3 13111.5 19175.0 23409.9 0.8 1.1 1.4 nephritis antigen-like 12 A0A061IKA1 Lipoprotein lipase 54.6 7.94 12714.5 12436.6 17956.6 20776.0 1.0 1.4 1.6 13 G3HQY6 Lipase 45.6 7.43 11294.8 10967.2 16138.6 19445.8 1.0 1.4 1.7 14 P62629 Elongation factor 1- 50.1 9.10 13770.0 14259.3 16568.8 19366.2 1.0 1.2 1.4 alpha 1 15 G318R9 78 kDa glucose- 72.3 5.01 10128.8 25865.6 41706.4 17820.4 2.6 4.1 1.8 regulated protein 16 G3GUR1 Complement C1r-A 80.0 5.64 5376.2 5637.8 11704.9 17444.1 1.0 2.2 3.2 subcomponent 17 G3HNF5 Papilin (Fragment) 127.2 7.27 463.9 490.3 4580.1 16039.8 1.1 9.9 34.6 18 G3GXZ0 Protein-glutamine 77.2 5.11 4526.0 6593.4 12121.1 14431.9 1.5 2.7 3.2 gamma- glutamyltransferase 2 19 G3I1Y9 Sulfated glycoprotein 1 27.4 5.35 4288.9 3455.4 6153.1 11892.6 0.8 1.4 2.8 20 A0A061I523 Procollagen C-endopeptidase 50.4 7.94 5237.6 5455.5 9859.9 11552.8 1.0 1.9 2.2 enhancer 1 21 G3HLK3 Granulins 63.9 5.97 1541.7 1771.4 7858.8 10614.2 1.1 5.1 6.9 22 G3HC84 Heat shock protein 47.8 5.32 3915.9 4483.9 9716.8 9920.4 1.1 2.5 2.5 HSP 90-beta 23 G3GUR0 Calcium-dependent 77.4 4.72 2204.4 2153.9 5351.9 9894.8 1.0 2.4 4.5 serine proteinase 24 G3HHV4 Thrombospondin-1 60.0 4.25 4163.8 4863.3 7442.9 9109.5 1.2 1.8 2.2 25 G3H1D5 Carboxypeptidase 51.2 5.30 4184.9 3967.5 6985.5 8678.0 0.9 1.7 2.1 26 G3IAQ0 Alpha-enolase 46.7 5.85 4290.5 4413.4 6823.4 8376.7 1.0 1.6 2.0 27 G3I4W7 Cathepsin D 44.1 6.59 3412.6 2873.9 4601.9 7320.9 0.8 1.3 2.1 28 G3HDL6 Elongation factor 1- 24.7 4.50 2857.1 7716.5 9131.7 7289.8 2.7 3.2 2.6 beta 29 G3H8V4 Phospholipid transfer 54.3 6.24 4397.5 3564.0 5887.0 7227.7 0.8 1.3 1.6 protein 30 G3HEI6 Lysyl oxidase-like 1 62.1 6.14 702.8 824.5 2371.9 6174.7 1.2 3.4 8.8 31 G3H3E2 Complement C1q 35.6 7.77 95.2 1153.6 5031.2 6131.5 12.1 52.9 64.4 tumor necrosis factor-related protein 1 32 A0A061I5D1 Heat shock cognate 70.6 5.37 2472.1 4204.9 7601.5 5286.1 1.7 3.1 2.1 protein 33 A0A061IEA0 Elongation factor 1- 72.9 6.66 1918.6 4159.7 5562.9 5180.7 2.2 2.9 2.7 delta-like isoform 1 34 G3HIQ1 Peptidyl-prolyl cis- 17.9 8.44 9127.8 7989.4 7293.1 4981.2 0.9 0.8 0.5 trans isomerase 35 A0A061I058 Elongation factor 1- 51.7 6.38 2770.1 4803.2 5660.0 4649.3 1.7 2.0 1.7 gamma 36 G3GTT2 C-C motif 15.8 9.39 1933.9 1795.2 3154.8 4609.6 0.9 1.6 2.4 chemokine 37 G3HRK9 Matrix 58.9 7.81 2621.2 2496.7 3902.4 4481.2 1.0 1.5 1.7 metalloproteinase-19 38 G3H3E4 Galectin-3-binding 63.8 5.05 4876.8 5402.7 3752.6 4400.0 1.1 0.8 0.9 protein 39 A0A098KXC0 Pyruvate kinase 81.4 8.59 2771.2 2823.6 3984.9 4374.1 1.0 1.4 1.6 40 G3HTE5 Lysosomal alpha- 105.8 5.65 2163.0 2207.5 3525.0 4352.6 1.0 1.6 2.0 glucosidase 41 Q9JKY1 Peroxiredoxin-1 22.2 8.21 3376.6 3373.7 4327.3 4331.9 1.0 1.3 1.3 42 G3H8F4 Dystroglycan 96.8 8.70 1733.3 1889.3 2976.1 4324.7 1.1 1.7 2.5 43 A0A061I2S4 Putative out at first 23.5 5.42 1138.2 1224.6 2957.2 4316.1 1.1 2.6 3.8 protein like protein (Fragment) 44 G3HBI1 Peroxidasin-like 165.3 6.49 1003.0 845.2 2640.4 4245.4 0.8 2.6 4.2 45 G3H0L9 Cathepsin B 37.5 5.73 2070.2 1615.1 2211.7 3850.9 0.8 1.1 1.9 46 G3IEB7 Out at first protein- 17.7 8.38 927.5 1002.5 2925.0 3843.2 1.1 3.2 4.1 like 47 G3HP49 Tetranectin 22.3 5.58 692.3 673.0 1734.3 3754.3 1.0 2.5 5.4 48 G3IDM2 Cofilin-1 18.5 8.22 2133.0 2177.6 2914.8 3634.8 1.0 1.4 1.7 49 G3HWE4 Nidogen-1 79.0 4.77 1316.4 1191.5 2274.9 3627.7 0.9 1.7 2.8 50 G3H3E6 Metalloproteinase 21.5 7.47 205.8 229.8 1196.4 3609.7 1.1 5.8 17.5 inhibitor 2

A parallel plot of relative abundance of mAb2 versus time revealed that some of the high abundant HCPs increased over time (See FIG. 26).

In order to understand the amounts of HCPs precipitated in the incubated CCF filter at different time points, a bubble plot of the ratio of abundance of the HCP at a time T/abundance of the HCP at TO versus relative amount of mAb2 LC at time T (ppm) is shown in FIG. 27 (T=0 hours), FIG. 28 (T=24 hours), FIG. 29 (T=48 hours), and FIG. 30 (T=72 hours). As seen in FIG. 28, a few of the HCPs (for example Complement C1q tumor necrosis, Elongation factor 1-beta, 78 kDa glucose-regulated protein and Elongation factor 1-delta-like isoform 1) increased over 2-fold which correlated to a moderated decrease in filter capacity. After 48 hours, a lot of the HCPs increased over 2-fold correlating to a similar significant decrease in filter capacity (See FIG. 29). At 72 hours, abundance at 72 hours for almost all of the top fifty HCPs increased over 2-fold compared to their abundance at 0 hour (See FIG. 30). For nine proteins form the top fifty HCPs increased over 5-fold compared to their abundance at 0 hour (Table 14).

Among the top fifty HCPs, Fibronectin showed a 4.6-fold increase at 72 hours and had the highest molecular weight and was possibly the most likely the cause of decreased filter capacity.

Sub-visible or visible particles can lead to decreased filter capacity and finding the root cause for formation of sub-visible or visible particles or the root cause for decrease in filter capacity can be imperative for drug products or bioprocesses. Once the cause has been identified, steps can be taken to avoid it. The methods described herein can facilitate the identification of the root cause of formation of visible and sub-visible particles. 

What is claimed is:
 1. A method for characterization of a protein in at least one visible or sub-visible particle in a sample, comprising: detecting the at least one visible or sub-visible particle in the sample; isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein; and using a mass spectrometer to characterize the protein.
 2. The method of claim 1, wherein the at least one visible or sub-visible particle is identified using a Raman spectroscopy.
 3. The method of claim 1, wherein the at least one visible or sub-visible particle has a size of at least about 100 μm.
 4. The method of claim 1, wherein the at least one visible or sub-visible particle is an inherent impurity.
 5. The method of claim 1, further comprising capturing the at least one visible or sub-visible particle on a gold-coated polycarbonate membrane.
 6. The method of claim 1, wherein the pore size of the gold-coated polycarbonate membrane is about 5 μm.
 7. The method of claim 1, further comprising dissolving the sample in urea after performing Raman spectroscopy analysis.
 8. The method of claim 6, wherein the concentration of urea is about 8 M.
 9. The method of claim 1, further comprising digesting the sample under denaturing conditions after performing Raman spectroscopy analysis.
 10. The method of claim 1, wherein the sample further comprises a protein of interest.
 11. The method of claim 9, wherein the protein of interest is an antibody.
 12. The method of claim 9, wherein the protein of interest is a therapeutic antibody.
 13. The method of claim 1, wherein the mass spectrometer is coupled to a liquid chromatography system.
 14. The method of claim 12, wherein the liquid chromatography system is a nano liquid chromatography system.
 15. The method of claim 1, wherein the mass spectrometer is a tandem mass spectrometer.
 16. The method of claim 1, wherein the protein is a host-cell protein.
 17. A method for quantification of at least one protein in at least one visible or sub-visible particle in a sample, comprising: detecting the at least one visible or sub-visible particle in the sample; isolating and capturing the at least one visible or sub-visible particle to identify a presence of the at least one protein; and identifying the at least one protein using a mass spectrometer.
 18. The method of claim 17, wherein the at least one protein is a host-cell protein.
 19. The method of claim 17, wherein the at least one visible or sub-visible particle is an aggregate of a protein.
 20. A method for characterization of a host cell-protein in at least one visible or sub-visible particle in a sample, comprising: detecting at least one visible or sub-visible particle in the sample; isolating and capturing the at least one visible or sub-visible particle to identify a presence of a protein; and using a mass spectrometer to characterize the protein to determine if the protein is the host cell-protein. 